Variant report

Variant	rs12029474
Chromosome Location	chr1:85793863-85793864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85783416..85785101-chr1:85792646..85795360,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12022538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12023006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12029684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12033170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs12033473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12034481	0.94[ASN][1000 genomes]
rs12036146	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038279	0.90[ASN][1000 genomes]
rs12039188	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12045545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046433	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047139	0.81[ASN][1000 genomes]
rs12047220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2300638	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28847138	0.98[ASN][1000 genomes]
rs3813603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485987	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap]
rs58489234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
2	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:85780400-85795800	Weak transcription	Gastric	stomach
6	chr1:85782400-85795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:85782800-85794600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:85783000-85795800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:85783200-85795800	Weak transcription	Aorta	Aorta
10	chr1:85784000-85794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:85784600-85794600	Weak transcription	Fetal Lung	lung
12	chr1:85788600-85797400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:85789400-85795800	Weak transcription	Liver	Liver
14	chr1:85789600-85794600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:85789800-85795800	Weak transcription	Fetal Stomach	stomach
16	chr1:85789800-85795800	Weak transcription	Lung	lung
17	chr1:85790000-85795600	Enhancers	NHDF-Ad	bronchial
18	chr1:85790200-85795200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:85790400-85795600	Weak transcription	Brain Germinal Matrix	brain
20	chr1:85790400-85796200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:85790400-85797000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:85790600-85794200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:85790600-85794400	Enhancers	Hela-S3	cervix
24	chr1:85790600-85800000	Enhancers	HUVEC	blood vessel
25	chr1:85790800-85794400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:85790800-85794600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:85791000-85794200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:85791000-85794200	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:85791000-85794600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:85791000-85796800	Enhancers	HepG2	liver
31	chr1:85791200-85794000	Weak transcription	Left Ventricle	heart
32	chr1:85791200-85794200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:85791200-85794800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:85791200-85798000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:85791400-85794400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:85791400-85794600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:85791400-85794800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:85791400-85797400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:85791800-85794600	Weak transcription	Fetal Intestine Large	intestine
40	chr1:85792000-85794400	Weak transcription	Fetal Heart	heart
41	chr1:85792000-85794600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:85792000-85795400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:85792000-85795800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:85792200-85795600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:85792200-85796400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:85792200-85806000	Weak transcription	Fetal Kidney	kidney
47	chr1:85792400-85794000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:85792400-85794400	Enhancers	A549	lung
49	chr1:85792400-85796200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:85792600-85794800	Weak transcription	Stomach Mucosa	stomach

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